Provide API to query for polymorphic and uncertain states #175
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This was referenced Oct 26, 2018
hlapp
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The algorithm implemented here keeps the previous mechanism for column type coercion, however it is now only applied for characters that don't have a polymorpic or uncertain state. Accomplishing this without depending on correctly second-guessing the symbol requires knowing for each state whether it is polymorphic, uncertain, or "standard". To not have do this work again if the user wants to have this knowledge as well, we return this on demand in the form of a second matrix whose columns are factors with levels `standard`, `polymorphic`, and `uncertain`. The matrix will have `NA` where the state is `NA`. Fixes #186. Closes #175.
cboettig
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…tes (#188) * Fixes type coercion for morphological characters with polymorphic states The algorithm implemented here keeps the previous mechanism for column type coercion, however it is now only applied for characters that don't have a polymorpic or uncertain state. Accomplishing this without depending on correctly second-guessing the symbol requires knowing for each state whether it is polymorphic, uncertain, or "standard". To not have do this work again if the user wants to have this knowledge as well, we return this on demand in the form of a second matrix whose columns are factors with levels `standard`, `polymorphic`, and `uncertain`. The matrix will have `NA` where the state is `NA`. Fixes #186. Closes #175. * Adds tests for obtaining state type matrix from get_characters * Regenerates man page for get_characters()
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To enable users to make their own decisions about how to code and how to count polymorphic and uncertain character states in downstream analysis, should provide an API along the following capabilities:
is_polymorphic()andis_uncertain(): predicate functions, would return a TRUE/FALSE matrix in the same arrangement as the character matrix.This is carved out from #172. Originally this included the ability to include member states as well, which is now moved to #187.
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